From ad63258b11ef452119a2ab3f5fbc084c50d78294 Mon Sep 17 00:00:00 2001
From: avahoffman <avamariehoffman@gmail.com>
Date: Thu, 16 May 2024 22:39:26 -0400
Subject: [PATCH] Add anvil image

---
 ottr_anvil/Dockerfile              | 78 ++++++++++++++++++++++++++++++
 ottr_anvil/github_package_list.tsv |  8 +++
 ottr_anvil/install_github.R        | 52 ++++++++++++++++++++
 3 files changed, 138 insertions(+)
 create mode 100644 ottr_anvil/Dockerfile
 create mode 100644 ottr_anvil/github_package_list.tsv
 create mode 100644 ottr_anvil/install_github.R

diff --git a/ottr_anvil/Dockerfile b/ottr_anvil/Dockerfile
new file mode 100644
index 0000000..04dc76f
--- /dev/null
+++ b/ottr_anvil/Dockerfile
@@ -0,0 +1,78 @@
+FROM rocker/tidyverse:4.4.0
+LABEL maintainer="avamariehoffman@gmail.com"
+WORKDIR /rocker-build/
+
+COPY install_github.R .
+
+# Install apt-getable packages to start
+RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialog
+RUN apt-get install -y --no-install-recommends \
+    libxt6 \
+    libpoppler-cpp-dev \
+    vim \
+    libglpk40 \
+    curl \
+    gpg
+
+# Install gh
+RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | gpg --dearmor -o /usr/share/keyrings/githubcli-archive-keyring.gpg;
+RUN echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null;
+RUN apt update && apt install -y gh;
+
+# Uninstall old version of pandoc
+RUN sudo apt-get purge pandoc pandoc-citeproc pandoc-data \
+  && sudo apt-get autoremove --purge
+
+# Install pandoc
+RUN wget https://github.com/jgm/pandoc/releases/download/2.14.1/pandoc-2.14.1-1-amd64.deb \
+  && sudo apt-get install ./pandoc-2.14.1-1-amd64.deb
+
+# Create new symlinks
+RUN ln -s /usr/bin/pandoc /usr/lib/rstudio-server/bin/pandoc
+
+# Add curl, bzip2
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+    bzip2 \
+    curl
+
+# Install pip3 and installation tools
+RUN apt-get -y --no-install-recommends install \
+    python3-pip  python3-dev
+
+RUN Rscript -e "remove.packages('rlang')"
+
+# Commonly used R packages
+RUN Rscript -e  "options(warn = 2);install.packages( \
+    c('rlang', \
+      'bookdown', \
+      'emojifont', \
+      'here', \
+      'leanpubr', \
+      'optparse', \
+      'oro.nifti', \
+      'qpdf', \
+      'R.utils', \
+      'rprojroot', \
+      'rgoogleslides', \
+      'servr', \
+      'spelling', \
+      'styler', \
+      'reticulate', \
+      'googlesheets4', \
+      'tibble'), \
+      repos = 'https://cloud.r-project.org/')"
+
+# cow needs this dependency:
+RUN Rscript -e  "devtools::install_version('gitcreds', version = '0.1.1', repos = 'http://cran.us.r-project.org')"
+
+# Copy over git token and package list
+COPY git_token.txt .
+COPY github_package_list.tsv .
+
+# Install packages from github
+RUN Rscript install_github.R \
+  --packages github_package_list.tsv \
+  --token git_token.txt
+
+# Set final workdir for commands
+WORKDIR /home/rstudio
diff --git a/ottr_anvil/github_package_list.tsv b/ottr_anvil/github_package_list.tsv
new file mode 100644
index 0000000..d25f995
--- /dev/null
+++ b/ottr_anvil/github_package_list.tsv
@@ -0,0 +1,8 @@
+rstudio/rmarkdown	HEAD
+yihui/xfun	HEAD
+yihui/knitr	HEAD
+jhudsl/ottrpal	HEAD
+tidyverse/rvest	4fe39fb5089512d77b6a9cc026e5c895258ff6ce
+R-lib/testthat	e99155af85261e065192feb946dcfa6679cffae4
+rstudio/bookdown	HEAD
+jhudsl/cow	HEAD
\ No newline at end of file
diff --git a/ottr_anvil/install_github.R b/ottr_anvil/install_github.R
new file mode 100644
index 0000000..fb532ec
--- /dev/null
+++ b/ottr_anvil/install_github.R
@@ -0,0 +1,52 @@
+#!/usr/bin/env Rscript
+
+if (!"optparse" %in% installed.packages()) {
+  install.packages("optparse")
+}
+
+library(optparse)
+
+################################ Set up options ################################
+# Set up optparse options
+option_list <- list(
+  make_option(
+    opt_str = c("-p", "--packages"), type = "character",
+    default = "github_package_list.tsv" ,
+    help = "Path to a TSV with a list of packages to be installed through Github, 
+    where file where the first column is the github package name e.g. 
+    jhudsl/ottrpal and the second column is the commit ID to be installed 
+    (to be supplied to the ref argument).
+    ",
+    metavar = "character"
+  ),
+  make_option(
+    opt_str = c("--token"), type = "character",
+    default = NULL,
+    help = "GITHUB PAT file",
+    metavar = "character"
+  )
+)
+
+# Parse options
+opt <- parse_args(OptionParser(option_list = option_list))
+
+# Read in the token
+token <- as.character(readLines(opt$token)[1])
+
+# Reset GITHUB PAT to be token
+Sys.unsetenv("GITHUB_PAT")
+Sys.setenv(GITHUB_PAT = token)
+
+# set up list of packages to install
+packages <- readr::read_tsv(opt$packages, 
+                                col_names = c("package_name", "ref"))
+
+purrr::pmap(
+  packages,
+  ~remotes::install_github(..1,
+                           auth_token = token,
+                           ref = ..2)
+                )
+
+# Remove the file after we are done
+file.remove(opt$token)